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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #321651

Title: Genome-environment associations in sorghum landraces predict adaptive traits

item LASKY, JESSE - Columbia University - New York
item UPADHYAYA, HARI - Kansas State University
item RAMU, PUNNA - Cornell University
item DESHPANDE, SHANTOSH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item HASH, THOMAS - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item BONNETTE, JASON - University Of Texas
item JUENGER, THOMAS - University Of Texas
item HYMA, KATIE - Cornell University
item ACHARYA, CHARLOTTE - Cornell University
item MITCHELL, SHARON - Cornell University
item Buckler, Edward - Ed
item BRENTON, ZACHARY - University Of South Carolina
item KRESOVICH, STEPHEN - University Of South Carolina
item MORRIS, GEOFFREY - University Of South Carolina

Submitted to: Science Advances
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/26/2015
Publication Date: 7/3/2015
Citation: Lasky, J.R., Upadhyaya, H.D., Ramu, P., Deshpande, S., Hash, T.C., Bonnette, J., Juenger, T., Hyma, K., Acharya, C., Mitchell, S.E., Buckler IV, E.S., Brenton, Z., Kresovich, S., Morris, G.P. 2015. Genome-environment associations in sorghum landraces predict adaptive traits. Life Science Advances. 1(6):e1400218.

Interpretive Summary: We identified the genomic signatures of local adaptation in sorghum, which can help to predict the behavior of plants in adverse environmental conditions. We demonstrated that environment explained a substantial proportion of variation in sorghum genome and these variations are enriched in genes which are expressed in response to hard-environmental conditions (E.g.: drought and aluminum tolerance). These signatures of environment associations will be useful for crop improvement by integrating with genome wide associations in selection to develop new plant varieties, which can withstand harsh climate changes to increase the crop/sorghum production to meet the global food demands in future.

Technical Abstract: Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.